Actually, as I have tried it several times. If you book separately, it will be treated as a separate booking with a different reservation number. So if it is a PC points preference it wont matter but if it is miles preference it will as you will get 500 miles X 2 for two separate bookings even on two consecutive nights. Plus if there are bonuses you are registered, you will also get both.

And yes if you are deligent enough to check your account, as soon as the first night posted ( if it is two separate bookings), you can then change the preference immediately and you will get the second night at your preference earning.

This will not be merged as one stay as these are two separate bookings. I have tried it so many times in different hotels ( HI/CP/IC).

This is similar in booking a reward stay if you choose to book ten nights one at a time. It will not be merged. And there's a reason doing this thing - so you can cancel an individual night if plan changes.